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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATAGTATGAGGAAAAGAAAATCACTAATGTCTGTAGAAGCTAAAGTTGGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatggtcacttgtcacaattcataactttctattatacgttaagtcaagactgtcctacatcatttgcagctttagtcacttactattagattaa...

Basic information

species Oryza sativa
transcript LOC_Os04g47240.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g47240.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G175504_T01 (Zea mays), 5'ss of exon 11
----ATCATAGTATGAGGAAAAGAAAATCACTAATGTCTGTAGAAGCTAA-AGTTGGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatggtcacttgtcacaattcataactttctattatacgttaagtcaag--actgtcctacatcatttgcagctttagtcacttactattagattaa-----
    |||||||||| || || |     |   |||| ||| ||||||||||  |||| |||||||||| |||| ||||||||||||| ||||||||||   |||||||||||     | ||| ||  ||||     || |   ||| |   |   ||||   ||   ||| |||       | || |  | | | |||   ||||| |     
GTGTATCATAGTATCAGAAAGA-----TTGATAATTTCTTTAGAAGCTAATGGTTGCCAATGGATGGGATCTCTGTTGTCATCAACGCAATTCAAGTCAACAAAGgtatgc-----cccttatcctaatttgcgcctgtt--ttacaatctgcatcaatttacgcacctgcatagggccaaactattctaaatcacttgcagattcagtgtc
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86869745|gb|CI322231.1|CI322231
EST:     ATCAACACAATTCAAG-TGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: ATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|86839941|gb|CI332632.1|CI332632
EST:     TTGTCATCAACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: TTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|86871440|gb|CI334371.1|CI334371
EST:     TTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: TTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|9866172|gb|AU101922.1|AU101922
EST:     GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|89186008|gb|CI047877.1|CI047877
EST:     GGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: GGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|66915330|gb|CX102178.1|CX102178
EST:     GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|88382539|gb|CI535747.1|CI535747
EST:     GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|29675826|gb|CB672101.1|CB672101
EST:     GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|86841287|gb|CI342998.1|CI342998
EST:     AATGGATGGAATCGTTGTTGTCATCAACACAATTCAAGGTGGCAAAG                         ATATCGTCCATTCCTGGTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: AATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|88831460|gb|CI083854.1|CI083854
EST:     GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|88845401|gb|CI084326.1|CI084326
EST:     AACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: AACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|88286600|gb|CI517711.1|CI517711
EST:     GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|86479295|gb|CI121928.1|CI121928
EST:     GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: GGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
EST: gi|86864116|gb|CI333985.1|CI333985
EST:     TCAACACAATTCAAGTTGGCAAAG                         ATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC
genomic: TCAACACAATTCAAGTTGGCAAAGgtatgcatgg ... taaatagcagATATCGTCCATTCCTGTTAGGCAGAACTCCCGGAAGCATACTACAATTGGC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATAGTATGAGGAAAAGAAAATCACTAATGTCTGTAGAAGCTAAAGTTGGCAATGGATGGAATCTTTGTTGTCATCAACACAATTCAAGTTGGCAAAGgtatgcatggtcacttgtcacaattcataactttctattatacgttaagtcaagactgtcctacatcatttgcagctttagtcacttactattagattaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG